Bio::Map::OrderedPosition(3pm) User Contributed Perl Documentation Bio::Map::OrderedPosition(3pm)
NAME
Bio::Map::OrderedPosition - Abstracts the notion of a member of an ordered list of markers. Each marker is a certain distance
from the one in the ordered list before it.
SYNOPSIS
use Bio::Map::OrderedPosition;
# the first marker in the sequence
my $position = Bio::Map::OrderedPosition->new(-order => 1,
-positions => [ [ $map, 22.3] ] );
# the second marker in the sequence, 15.6 units from the fist one
my $position2 = Bio::Map::OrderedPosition->new(-order => 2,
-positions => [ [ $map, 37.9] ] );
# the third marker in the sequence, coincidental with the second
# marker
my $position3 = Bio::Map::OrderedPosition->new(-order => 3,
-posititions => [ [ $map, 37.9]] );
DESCRIPTION
This object is an implementation of the PositionI interface and the Position object handles the specific values of a position.
OrderedPosition is intended to be slightly more specific then Position but only specific enough for a parser from the MarkerIO subsystem to
create and then pass to a client application to bless into the proper type. For an example of how this is intended to work, see the
Mapmaker.pm.
No units are assumed here - units are handled by context of which Map a position is placed in.
Se Bio::Map::Position for additional information.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Chad Matsalla
Email bioinformatics1@dieselwurks.com
CONTRIBUTORS
Lincoln Stein, lstein@cshl.org Heikki Lehvaslaiho, heikki-at-bioperl-dot-org Jason Stajich, jason@bioperl.org Sendu Bala, bix@sendu.me.uk
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : my $obj = Bio::Map::OrderedPosition->new();
Function: Builds a new Bio::Map::OrderedPosition object
Returns : Bio::Map::OrderedPosition
Args : -order : The order of this position
order
Title : order
Usage : $o_position->order($new_order);
my $order = $o_position->order();
Function: Get/set the order position of this position in a map.
Returns : int, the order of this position
Args : none to get, OR int to set
sortable
Title : sortable
Usage : my $num = $position->sortable();
Function: Read-only method that is guaranteed to return a value suitable
for correctly sorting this kind of position amongst other positions
of the same kind on the same map. Note that sorting different kinds
of position together is unlikely to give sane results.
Returns : numeric
Args : none
equals
Title : equals
Usage : if ($mappable->equals($mapable2)) {...}
Function: Test if a position is equal to another position.
Returns : boolean
Args : Bio::Map::PositionI
less_than
Title : less_than
Usage : if ($mappable->less_than($m2)) {...}
Function: Tests if a position is less than another position
It is assumed that 2 positions are in the same map.
Returns : boolean
Args : Bio::Map::PositionI
greater_than
Title : greater_than
Usage : if ($mappable->greater_than($m2)) {...}
Function: Tests if position is greater than another position.
It is assumed that 2 positions are in the same map.
Returns : boolean
Args : Bio::Map::PositionI
perl v5.14.2 2012-03-02 Bio::Map::OrderedPosition(3pm)